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branches/nemo_v3_3_beta/DOC/TexFiles/Chapters/Chap_MISC.tex
r2282 r2349 22 22 Mediterranean to replenish its supply of water from the Atlantic to balance the net 23 23 evaporation occurring over the Mediterranean region. This problem occurs even in 24 eddy permitting simulations. For example, in ORCA 1/4\ r{}several straits of the Indonesian24 eddy permitting simulations. For example, in ORCA 1/4\deg several straits of the Indonesian 25 25 archipelago (Ombai, Lombok...) are much narrow than even a single ocean grid-point. 26 26 … … 33 33 Note that such modifications are so specific to a given configuration that no attempt 34 34 has been made to set them in a generic way. However, examples of how 35 they can be set up is given in the ORCA 2\ r{} and 0.5\r{}configurations (search for36 \key{ ORCA\_R2} or \key{ORCA\_R05} in the code).35 they can be set up is given in the ORCA 2\deg and 0.5\deg configurations (search for 36 \key{orca\_r2} or \key{orca\_r05} in the code). 37 37 38 38 % ------------------------------------------------------------------------------------------------------------- … … 61 61 \includegraphics[width=0.80\textwidth]{./TexFiles/Figures/Fig_Gibraltar.pdf} 62 62 \includegraphics[width=0.80\textwidth]{./TexFiles/Figures/Fig_Gibraltar2.pdf} 63 \caption {Example of the Gibraltar strait defined in a 1\r{} x 1\r{}mesh.63 \caption {Example of the Gibraltar strait defined in a $1\deg \times 1\deg$ mesh. 64 64 \textit{Top}: using partially open cells. The meridional scale factor at $v$-point 65 65 is reduced on both sides of the strait to account for the real width of the strait … … 144 144 % 1D model functionality 145 145 % ================================================================ 146 \section{Water column model: 1D model (\key{c fg\_1d})}146 \section{Water column model: 1D model (\key{c1d})} 147 147 \label{MISC_1D} 148 148 149 149 The 1D model option simulates a stand alone water column within the 3D \NEMO system. 150 150 It can be applied to the ocean alone or to the ocean-ice system and can include passive tracers 151 or a biogeochemical model. It is set up by defining the \key{c fg\_1d} CPP key.151 or a biogeochemical model. It is set up by defining the \key{c1d} CPP key. 152 152 The 1D model is a very useful tool 153 153 \textit{(a)} to learn about the physics and numerical treatment of vertical mixing processes ; … … 226 226 % \gmcomment{why not make these bullets into subsections?} 227 227 228 Three issues to be described here: 229 230 $\bullet$ Vector and memory optimisation: 228 229 $\bullet$ Vector optimisation: 231 230 232 231 \key{vectopt\_loop} enables the internal loops to collapse. This is very … … 237 236 238 237 % Add also one word on NEC specific optimisation (Novercheck option for example) 239 240 \key{vectopt\_memory} is an obsolescent option. It has been introduced in order241 to reduce the memory requirement of the model at a time when in-core memory242 were rather limited. This is obviously done at the cost of increasing the CPU243 time requirement, since it suppress intermediate computations which would have244 been saved in in-core memory. Currently it is only used in the old implementation245 of the TKE physics (\key{tke\_old}) where, when \key{vectopt\_memory}246 is defined, the coefficients used for horizontal smoothing of $A_v^T$ and $A_v^m$247 are no longer computed once and for all. This reduces the memory requirement by three248 3D arrays. This option will disappear in the next \NEMO release.249 250 238 251 239 $\bullet$ Control print %: describe here 4 things: … … 514 502 % Diagnostics 515 503 % ================================================================ 516 \section{Diagnostics (DIA, IOM )}504 \section{Diagnostics (DIA, IOM, TRD, FLO)} 517 505 \label{MISC_diag} 518 506 … … 520 508 % Standard Model Output 521 509 % ------------------------------------------------------------------------------------------------------------- 522 \subsection{ Standard Model Output (default option or \key{dimg})}510 \subsection{Model Output (default or \key{iomput} or \key{dimgout})} 523 511 \label{MISC_iom} 524 512 … … 551 539 flexibility in the choice of the fields to be output as well as how the 552 540 writing work is distributed over the processors in massively parallel 553 computing. It is activated when \key{ dimgout} is defined.541 computing. It is activated when \key{iomput} is defined. 554 542 555 543 % ------------------------------------------------------------------------------------------------------------- 556 544 % Tracer/Dynamics Trends 557 545 % ------------------------------------------------------------------------------------------------------------- 558 \subsection[Tracer/Dynamics Trends ( \key{trdlmd}, \textbf{key\_diatrd...})]559 {Tracer/Dynamics Trends (\key{trd lmd}, \key{diatrdtra}, \key{diatrddyn})}546 \subsection[Tracer/Dynamics Trends (TRD)] 547 {Tracer/Dynamics Trends (\key{trdmld}, \key{trdtra}, \key{trddyn}, \key{trdmld\_trc})} 560 548 \label{MISC_tratrd} 561 549 562 %to be udated this corresponds to OPA8 563 When \key{diatrddyn} and/or \key{diatrddyn} cpp variables are defined, each 550 %------------------------------------------namtrd---------------------------------------------------- 551 \namdisplay{namtrd} 552 %------------------------------------------------------------------------------------------------------------- 553 554 When \key{trddyn} and/or \key{trddyn} CPP variables are defined, each 564 555 trend of the dynamics and/or temperature and salinity time evolution equations 565 556 is stored in three-dimensional arrays just after their computation ($i.e.$ at the end 566 of each $dyn\cdots .F90$ and/or $tra\cdots .F90$ routine). These trends are then 567 used in diagnostic routines $diadyn.F90$ and $diatra.F90$ respectively. 568 In the standard model, these routines check the basin averaged properties of 569 the momentum and tracer equations every \textit{ntrd } time-steps (\textbf{namelist 570 parameter}). These routines are supplied as an example; they must be adapted by 571 the user to his/her requirements. 572 573 These two options imply the creation of several extra arrays in the in-core 574 memory, increasing quite seriously the code memory requirements. 557 of each $dyn\cdots.F90$ and/or $tra\cdots.F90$ routines). These trends are then 558 used in \mdl{trdmod} (see TRD directory) every \textit{nn\_trd } time-steps. 559 560 What is done depends on the CPP keys defined: 561 \begin{description} 562 \item[\key{trddyn}, \key{trdtra}] : a check of the basin averaged properties of the momentum 563 and/or tracer equations is performed ; 564 \item[\key{trdvor}] : a vertical summation of the moment tendencies is performed, 565 then the curl is computed to obtain the barotropic vorticity tendencies which are output ; 566 \item[\key{trdmld}] : output of the tracer tendencies averaged vertically 567 either over the mixed layer (\np{nn\_ctls}=0), 568 or over a fixed number of model levels (\np{nn\_ctls}$>$1 provides the number of level), 569 or over a spatially varying but temporally fixed number of levels (typically the base 570 of the winter mixed layer) read in \ifile{ctlsurf\_idx} (\np{nn\_ctls}=1). 571 \end{description} 572 573 The units in the output file can be changed using the \np{nn\_ucf} namelist parameter. 574 For example, in case of salinity tendency the units are given by PSU/s/\np{nn\_ucf}. 575 Setting \np{nn\_ucf}=86400 provides the tendencies in PSU/d. 576 577 When \key{trdmld} is defined, two time averaging procedure are proposed. 578 Setting \np{ln\_trdmld\_instant} to \textit{true}, a simple time averaging is performed, 579 so that the resulting tendency is the contribution to the change of a quantity between 580 the two instantaneous values taken at the extremities of the time averaging period. 581 Setting \np{ln\_trdmld\_instant} to \textit{false}, a double time averaging is performed, 582 so that the resulting tendency is the contribution to the change of a quantity between 583 two \textit{time mean} values. The later option requires the use of an extra file, \ifile{restart\_mld} 584 (\np{ln\_trdmld\_restart}=true), to restart a run. 585 586 587 Note that the mixed layer tendency diagnostic can also be used on biogeochemical models 588 via Êthe \key{trdtrc} and \key{trdmld\_trc} CPP keys. 575 589 576 590 % ------------------------------------------------------------------------------------------------------------- 577 591 % On-line Floats trajectories 578 592 % ------------------------------------------------------------------------------------------------------------- 579 \subsection{On-line Floats trajectories (FLO) }593 \subsection{On-line Floats trajectories (FLO) (\key{floats}} 580 594 \label{FLO} 581 595 %--------------------------------------------namflo------------------------------------------------------- … … 583 597 %-------------------------------------------------------------------------------------------------------------- 584 598 585 The on-line computation of floats ad evected either by the three dimensional velocity599 The on-line computation of floats advected either by the three dimensional velocity 586 600 field or constraint to remain at a given depth ($w = 0$ in the computation) have been 587 introduced in the system during the CLIPPER project. The algorithm used is based on 588 the work of \cite{Blanke_Raynaud_JPO97}. (see also the web site describing the off-line 589 use of this marvellous diagnostic tool (http://stockage.univ-brest.fr/~grima/Ariane/). 601 introduced in the system during the CLIPPER project. The algorithm used is based 602 either on the work of \cite{Blanke_Raynaud_JPO97} (default option), or on a $4^th$ 603 Runge-Hutta algorithm (\np{ln\_flork4}=true). Note that the \cite{Blanke_Raynaud_JPO97} 604 algorithm have the advantage of providing trajectories which are consistent with the 605 numeric of the code, so that the trajectories never intercept the bathymetry. 606 607 See also the web site describing the off-line use of this marvellous diagnostic tool 608 (http://stockage.univ-brest.fr/~grima/Ariane/). 590 609 591 610 % ------------------------------------------------------------------------------------------------------------- 592 611 % Other Diagnostics 593 612 % ------------------------------------------------------------------------------------------------------------- 594 \subsection{Other Diagnostics }613 \subsection{Other Diagnostics (\key{diahth}, \key{diaar5})} 595 614 \label{MISC_diag_others} 596 615 597 %To be updated this mainly corresponds to OPA 8598 616 599 617 Aside from the standard model variables, other diagnostics can be computed 600 on-line or can be added to the model. The available ready-to-add diagnostics 601 routines can be found in directory DIA. Among the available diagnostics are: 602 603 - the mixed layer depth (based on a density criterion) (\mdl{diamxl}) 604 605 - the turbocline depth (based on a turbulent mixing coefficient criterion) (\mdl{diamxl}) 606 607 - the depth of the 20\r{}C isotherm (\mdl{diahth}) 618 on-line. The available ready-to-add diagnostics routines can be found in directory DIA. 619 Among the available diagnostics the following ones are obtained when defining 620 the \key{diahth} CPP key: 621 622 - the mixed layer depth (based on a density criterion, \citet{de_Boyer_Montegut_al_JGR04}) (\mdl{diahth}) 623 624 - the turbocline depth (based on a turbulent mixing coefficient criterion) (\mdl{diahth}) 625 626 - the depth of the 20\deg C isotherm (\mdl{diahth}) 608 627 609 628 - the depth of the thermocline (maximum of the vertical temperature gradient) (\mdl{diahth}) 610 629 611 - the meridional heat and salt transports and their decomposition (\mdl{diamfl}) 630 The poleward heat and salt transports, their advective and diffusive component, and 631 the meriodional stream function can be computed on-line in \mdl{diaptr} by setting 632 \np{ln\_diaptr} to true (see the \textit{namptr} namelist below). 633 When \np{ln\_subbas}~=~true, transports and stream function are computed 634 for the Atlantic, Indian, Pacific and Indo-Pacific Oceans (defined north of 30\deg S) 635 as well as for the World Ocean. The sub-basin decomposition requires an input file 636 (\ifile{subbasins}) which contains three 2D mask arrays, the Indo-Pacific mask 637 been deduced from the sum of the Indian and Pacific mask (Fig~\ref{Fig_mask_subasins}). 638 639 %------------------------------------------namptr---------------------------------------------------- 640 \namdisplay{namptr} 641 %------------------------------------------------------------------------------------------------------------- 642 %>>>>>>>>>>>>>>>>>>>>>>>>>>>> 643 \begin{figure}[!t] \label{Fig_mask_subasins} \begin{center} 644 \includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_mask_subasins.pdf} 645 \caption {Decomposition of the World Ocean (here ORCA2) into sub-basin used in to compute 646 the heat and salt transports as well as the meridional stream-function: Atlantic basin (red), 647 Pacific basin (green), Indian basin (bleue), Indo-Pacific basin (bleue+green). 648 Note that semi-enclosed seas (Red, Med and Baltic seas) as well as Hudson Bay 649 are removed from the sub-basin. Note also that the Arctic Ocean has been split 650 into Atlantic and Pacific basins along the North fold line. } 651 \end{center} \end{figure} 652 %>>>>>>>>>>>>>>>>>>>>>>>>>>>> 612 653 613 654 In addition, a series of diagnostics has been added in the \mdl{diaar5}. … … 771 812 the \key{diaar5} defined to be called. 772 813 814 815 % ================================================================ 816 % predefined configurations 817 % ================================================================ 818 \section{predefined configurations} 819 \label{MISC_config} 820 821 There is several predefined ocean configuration which use is controlled by a specific CPP key. 822 823 The key set the domain sizes (\jp{jpiglo}, \jp{jpjglo}, \jp{jpk}), the mesh and the bathymetry, 824 and, in some cases, add to the model physics some specific treatments. 825 826 % ------------------------------------------------------------------------------------------------------------- 827 % ORCA family configurations 828 % ------------------------------------------------------------------------------------------------------------- 829 \subsection{ORCA family: global ocean with tripolar grid} 830 \label{MISC_config_orca} 831 832 The NEMO system is provided with four built-in ORCA configurations which differ in the 833 horizontal resolution used: 834 \begin{description} 835 \item[\key{orca\_r4}] \jp{cp\_cfg}~=~orca ; \jp{jp\_cfg}~=~4 836 \item[\key{orca\_r2}] \jp{cp\_cfg}~=~orca ; \jp{jp\_cfg}~=~2 837 \item[\key{orca\_r1}] \jp{cp\_cfg}~=~orca ; \jp{jp\_cfg}~=~1 838 \item[\key{orca\_r05}] \jp{cp\_cfg}~=~orca ; \jp{jp\_cfg}~=~05 839 \item[\key{orca\_r025}] \jp{cp\_cfg}~=~orca ; \jp{jp\_cfg}~=~025 840 \end{description} 841 842 \subsubsection{ORCA mesh} 843 844 %>>>>>>>>>>>>>>>>>>>>>>>>>>>> 845 \begin{figure}[!t] \label{Fig_MISC_ORCA_msh} \begin{center} 846 \includegraphics[width=0.98\textwidth]{./TexFiles/Figures/Fig_ORCA_NH_mesh.pdf} 847 \caption {ORCA mesh conception. The departure from an isotropic Mercator grid start poleward of 20\deg N. 848 The two "north pole" are the foci of a series of embedded ellipses (blue curves) 849 which are determined analytically and form the i-lines of the ORCA mesh (pseudo latitudes). 850 Then, following \citet{Madec_Imbard_CD96}, the normal to the series of ellipses (red curves) is computed 851 which provide the j-lines of the mesh (pseudo longitudes). 852 } 853 \end{center} \end{figure} 854 %>>>>>>>>>>>>>>>>>>>>>>>>>>>> 855 856 857 %>>>>>>>>>>>>>>>>>>>>>>>>>>>> 858 \begin{figure}[!tbp] \label{Fig_MISC_ORCA_e1e2} \begin{center} 859 \includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_ORCA_NH_msh05_e1_e2.pdf} 860 \includegraphics[width=0.80\textwidth]{./TexFiles/Figures/Fig_ORCA_aniso.pdf} 861 \caption {\textit{Top}: Horizontal scale factors ($e_1$, $e_2$) and 862 \textit{Bottom}: ratio of anisotropy ($e_1 / e_2$) 863 for ORCA 0.5\deg ~mesh. South of 20\deg N a Mercator grid is used ($e_1 = e_2$) 864 so that the anisotropy ratio is 1. Poleward of 20\deg N, the two "north pole" 865 introduce a weak anisotropy over the ocean areas ($< 1.2$) except in vicinity of Victoria Island 866 (Canadian Arctic Archipelago). } 867 \end{center} \end{figure} 868 %>>>>>>>>>>>>>>>>>>>>>>>>>>>> 869 870 %--------------------------------------------------TABLE-------------------------------------------------- 871 \begin{table}[htbp] \label{Tab_ORCA} 872 \begin{center} 873 \begin{tabular}{ccccc} 874 key & \jp{jp\_cfg} & \jp{jpiglo} & \jp{jpiglo} & \\ 875 \hline \hline 876 \key{orca\_r4} & 4 & 92 & 76 & \\ 877 \key{orca\_r2} & 2 & 182 & 149 & \\ 878 %\key{orca\_r1} & 1 & 362 & 511 & \\ 879 \key{orca\_r05} & 05 & 722 & 261 & \\ 880 \key{orca\_r025} & 025 & 1442 & 1021 & \\ 881 %\key{orca\_r8} & 8 & 2882 & 2042 & \\ 882 %\key{orca\_r12} & 12 & 4322 & 3062 & \\ 883 \hline 884 \hline 885 \end{tabular} 886 \caption {Set of predefined ORCA parameters. } 887 \end{center} 888 \end{table} 889 %-------------------------------------------------------------------------------------------------------------- 890 891 The tripolar grid used in ORCA configuration .... 892 893 NB: the two north poles position has been chosen to minimise the anisotropy ratio in 894 the Gulf Stream and kuroshio areas, two highly turbulent regions. 895 896 ORCA~2 : a $2\deg$ zonal resolution, and a meridional resolution varying from $0.5\deg$ at the 897 equator to $2\deg cos\phi$ south of $20\deg$S (Fig. 1). The grid features two points of convergence in the 898 Northern Hemisphere, both situated on continents. Minimum resolution in high latitudes is about 899 65~km in the Arctic and 50~km in the Antarctic. Local mesh refinements are applied to the 900 Mediterranean, Red, Black and Caspian Seas. None of them appears to be of particular 901 importance for the study of high latitude climate, but the fine resolution is needed in order to have 902 their local circulation and their role in the World Ocean's circulation considered correctly. 903 904 905 906 ORCA2-LIM (global ocean sea-ice configuration \citep{Timmermann_al_OM05}. 907 The horizontal mesh is based on a $2\deg \times 2\deg$ Mercator grid ($i.e.$ same zonal and 908 meridional grid spacing) which has been modified poleward 909 of $20\deg$N in order to include two numerical inland poles \citep{Murray_JCP96}. 910 This modification is semi-analytical \citep{Madec_Imbard_CD96} 911 and based on a series of embedded ellipses. It insures that the mesh remains 912 close to isotropy and that the smallest grid cell is along Antarctica. 913 In order to refine the meridional resolution up to $0.5\deg$ at the equator, 914 additional local transformations were applied with in the Tropics. 915 Local mesh refinements are also applied to the Mediterranean, Red, Black 916 and Caspian Seas so that the resolution is $1\deg \time 1\deg$ there. 917 There are 31 levels in the vertical, with the highest resolution (10m) 918 in the upper 150m. The bottom topography and the coastlines are derived 919 from the global atlas of Smith and Sandwell (1997). 920 921 \key{orca\_lev10} 10 time more vertical levels 922 923 \key{agrif} : ORCA2-LIM plus an AGRIF zoom over the Agulhas current area 924 925 \key{arctic}, \key{antarctic} (not used in ORCA\_R4) 926 927 928 We thus only provide a brief introduction in this chapter. 929 The global coupled ocean-ice configuration is very similar to that used as part of the climate 930 model developed at GFDL for the 4th IPCC assessment of climate change (Griffies et al., 2005; 931 Gnanadesikan et al., 2006). 932 The ORCA2-LIM configuration is also the basis for the \NEMO contribution to the 933 Coordinate Ocean-ice Reference Experiments (COREs) documented in \citet{Griffies_al_OM09}. 934 These experiments employ the boundary forcing from \citet{Large_Yeager_Rep04} (see \S\ref{SBC_blk_core}), 935 which was developed for the purpose of running global coupled ocean-ice simulations without an 936 interactive atmosphere. This \citet{Large_Yeager_Rep04} dataset is available through the GFDL web 937 site \footnote{http://nomads.gfdl.noaa.gov/nomads/forms/mom4/CORE.html}. 938 The "normal year" of \citet{Large_Yeager_Rep04} has been chosen of the \NEMO distribution 939 since release v3.3. 940 941 % ------------------------------------------------------------------------------------------------------------- 942 % GYRE family configuration 943 % ------------------------------------------------------------------------------------------------------------- 944 \subsection{GYRE family: double gyre basin (\key{gyre})} 945 \label{MISC_config_gyre} 946 947 The GYRE configuration \citep{Levy_al_OM10} have been built to simulated 948 the seasonal cycle of a double-gyre box model. It consist in an idealized domain 949 similar to that used in the studies of \citet{Drijfhout_JPO94} and \citet{Hazeleger_Drijfhout_JPO98, 950 Hazeleger_Drijfhout_JPO99, Hazeleger_Drijfhout_JGR00, Hazeleger_Drijfhout_JPO00}, 951 over which an analytical seasonal forcing is applied. This allows to investigate the 952 spontaneous generation of a large number of interacting, transient mesoscale eddies 953 and their contribution to the large scale circulation. 954 955 The domain geometry is a closed rectangular basin on the $\beta$-plane centred 956 at $\sim 30\deg$N and rotated by 45\deg, 3180~km long, 2120~km wide 957 and 4~km deep (Fig.~\ref{Fig_MISC_strait_hand}). 958 The domain is bounded by vertical walls and by a ßat bottom. The configuration is 959 meant to represent an idealized North Atlantic or North Pacific basin. 960 The circulation is forced by analytical profiles of wind and buoyancy ßuxes. 961 The applied forcings vary seasonally in a sinusoidal manner between winter 962 and summer extrema \citep{Levy_al_OM10}. 963 The wind stress is zonal and its curl changes sign at 22\deg N and 36\deg N. 964 It forces a subpolar gyre in the north, a subtropical gyre in the wider part of the domain 965 and a small recirculation gyre in the southern corner. 966 The net heat ßux takes the form of a restoring toward a zonal apparent air 967 temperature profile. A portion of the net heat ßux which comes from the solar radiation 968 is allowed to penetrate within the water column. 969 The fresh water ßux is also prescribed and varies zonally. 970 It is determined such as, at each time step, the basin-integrated ßux is zero. 971 The basin is initialised at rest with vertical profiles of temperature and salinity 972 uniformly applied to the whole domain. 973 974 The GYRE configuration is set through the \key{gyre} CPP key. Its horizontal resolution 975 (and thus the size of the domain) is determined by setting \jp{jp\_cfg} in \hf{par\_GYRE} file: \\ 976 \jp{jpiglo} $= 30 \times$ \jp{jp\_cfg} + 2 \\ 977 \jp{jpjglo} $= 20 \times$ \jp{jp\_cfg} + 2 \\ 978 Obviously, the namelist parameters have to be adjusted to the chosen resolution. 979 In the vertical, GYRE uses the default 30 ocean levels (\jp{jpk}=31) (Fig.~\ref{Fig_zgr}). 980 981 The GYRE configuration is also used in benchmark test as it is very simple to increase 982 its resolution and as it does not requires any input file. For example, keeping a same model size 983 on each processor while increasing the number of processor used is very easy, even though the 984 physical integrity of the solution can be compromised. 985 986 %>>>>>>>>>>>>>>>>>>>>>>>>>>>> 987 \begin{figure}[!t] \label{Fig_GYRE} \begin{center} 988 \includegraphics[width=1.0\textwidth]{./TexFiles/Figures/Fig_GYRE.pdf} 989 \caption {Snapshot of relative vorticity at the surface of the model domain 990 in GYRE R9, R27 and R54. From \citet{Levy_al_OM10}.} 991 \end{center} \end{figure} 992 %>>>>>>>>>>>>>>>>>>>>>>>>>>>> 993 994 % ------------------------------------------------------------------------------------------------------------- 995 % EEL family configuration 996 % ------------------------------------------------------------------------------------------------------------- 997 \subsection{EEL family: periodic channel} 998 \label{MISC_config_EEL} 999 1000 \begin{description} 1001 \item[\key{eel\_r2}] 1002 \item[\key{eel\_r5}] 1003 \item[\key{eel\_r6}] 1004 \end{description} 1005 1006 % ------------------------------------------------------------------------------------------------------------- 1007 % POMME configuration 1008 % ------------------------------------------------------------------------------------------------------------- 1009 \subsection{POMME: mid-latitude sub-domain} 1010 \label{MISC_config_POMME} 1011 1012 1013 \key{pomme\_r025} 1014 1015 1016
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